Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: DEX, 24hr. Homo sapiens

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools. Overall design: Total RNA from cultured trabecular bone cells obtained from ~100 unrelated Caucasian donors treated under multiple different conditions and timepoints. Each sample represented by two or three biological replicates. This dataset includes samples treated with dexamethasone (DEX) for 24 hours.

可改变正常基因表达顺式调控的遗传变异（顺式表达数量性状位点，cis-eQTLs）已在人类细胞及组织中被广泛定位，但截至目前，尚无研究探讨环境扰动对这类性状的影响程度。
我们针对113名无亲缘关系的瑞典籍供者来源的原代人骨细胞，开展了大规模诱导实验，实验共设置18种培养条件（7种处理因素、2种溶剂对照，每种条件均设置两个时间点进行检测）。
经两套独立表达芯片验证后，对转录组影响最显著的处理因素包括骨形态发生蛋白2（BMP-2，处理2小时）、地塞米松（DEX，处理24小时）及前列腺素E2（PGE2，处理24小时）。
基于上述处理因素，我们利用完整研究队列的生物学重复样本（总样本量n_total=782），对18144个RefSeq转录本进行了表达谱分析，并结合全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型数据，以定位处理因素特异性的顺式表达数量性状位点。
我们发现，在错误发现率（False Discovery Rate, FDR）为1%的条件下，93%的顺式表达数量性状位点可在至少一种其他处理因素中被重复验证；实际上，平均仅有1.4%的顺式表达数量性状位点可被判定为高置信度的处理因素特异性位点。
全基因组等位基因表达检测独立验证了扰动后顺式调控的相对稳定性：仅极小部分表达变异可归因于处理因素，不过在上调或下调的基因中，处理因素特异性顺式调控效应的丰度要高出2至6倍。
我们进一步对地塞米松特异性的MYO6与TNC基因座顺式调控进行了追踪验证，发现其顶级顺式调控变异分别位于转录起始位点上游180kb与250kb处。
我们的研究结果表明，与顺式表达数量性状位点的组织特异性不同，细胞环境与顺式变异之间的交互作用相对罕见（约占1.5%），但通过功能基因组学工具的联合应用，即可实现这类特异性交互作用的检测。
整体实验设计：本数据集源自约100名无亲缘关系的高加索供者来源的培养小梁骨细胞，经多种不同处理条件与时间点处理后提取总RNA；每份样本设置2至3个生物学重复。本数据集包含经地塞米松（DEX）处理24小时的样本。